~ Man and his will to survive!

Atom Typing with the CDK

Atom typing is an important and integral part of any chemoinformatics software. Most of the calculations, and more importantly the assignment of implicit/explicit hydrogen(s) depend on this. Thanks to Egon, Rajarshi and others, the CDK has improved a lot over the years.

I (with Nimish a summer intern) did a quick test on the KEGG molecules (before KEGG becomes a paid service on 30th June, which is a pity…..!).

The good news is that only 1.37% molecules failed the “Atom Typing” test, as compared to last year (the failure rate was approximately 10%, mostly phosphates). Most of the failed atoms are metals (Cl,N,S,Fe,Mn,Zn,Cu, etc).